TB-Profiler result

Run: SRR10869064

Summary

Run ID: SRR10869064

Sample name:

Date: 02-04-2023 19:37:54

Number of reads: 443645

Percentage reads mapped: 98.97

Strain: lineage2.2.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
gid 4407899 p.Arg102* stop_gained 0.15 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8459 c.1158G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 765192 p.Glu608Gly missense_variant 0.17
rpoC 766294 c.2925C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471675 n.-171G>A upstream_gene_variant 0.11
rpsA 1833682 c.141C>T synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155042 p.Asp357Gly missense_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714578 p.Leu252Ser missense_variant 0.17
pepQ 2860018 p.Val134Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339486 c.369G>A synonymous_variant 0.13
Rv3083 3448478 c.-25delG upstream_gene_variant 0.11
Rv3083 3448503 c.-1C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474529 p.Arg175Cys missense_variant 0.11
fprA 3475139 p.Thr378Ile missense_variant 0.14
Rv3236c 3612061 c.1056C>T synonymous_variant 0.18
Rv3236c 3612472 c.645C>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612950 p.Glu56Val missense_variant 0.14
alr 3840693 p.Arg243His missense_variant 0.11
embC 4242474 p.Leu871Pro missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245705 p.His825Tyr missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407827 p.Asp126Tyr missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0